lecture 5

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Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 1 WHEN WE ENDED LAST TIME WE HAD JUST LISTED THE THINGS THAT PROTEINS DO What is it about proteins that allows them to have all these properties and more? Proteins are linear polymers of building blocks called amino acids. Their properties depend entirely on the collective properties of the amino acids in a protein, and the order in which they are there. This sets the 3D shape of the protein. So, we need to understand something of the properties of amino acids. Amino acids have the general structure: Amino acids never have this form in solution. Why not? Look at the simplest amino acid, glycine (R = H). Its different forms are in equilibrium We will examine their acid/base properties later. Amino acids have chiral centers; that is, they are asymmetric. They can exist as stereoisomers.

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 2 The isomers are categorized with reference to glyceraldehyde, the simplest sugar to have an asymmetric C atom. All amino acids in proteins are L stereoisomers. This arises from the exquisite sensitivity of the active sites of enzymes to 3d structures. D-amino acids occur in nature, but not in proteins. The building blocks of proteins are hooked together via the peptide bond . Because the peptide bond has partial double bond character , it is planar .

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 3 This imparts some important properties to proteins, which we will see later. Since amino acids all have the  amino and carboxyl groups, the peptide bond can, in principle, be formed in either direction. This is why proteins are linear polymers of amino acids joined by peptide bonds. Recall the general structure of an amino acid in the neutral pH form: Proteins are made from 20 different L-amino acids. The amino acids can be grouped together in many different ways, and we'll go through the using the grouping from Lehninger. In order to facilitate writing them down, amino acids have been given abbreviations. There are individual three-letter and one-letter abbreviations, which you must learn. For instance, Glycine is abbreviated Gly or G. Not always easy. For instance, Glutamine is abbreviated Gln or Q. I will give you the long, three letter abbrev and the one letter abbrev. I will also give you a number that corresponds to the hydrophobicity of the amino acid. There are a couple of scales that can be used, and I’ll just pick one. In this scale, plus = hydrophobic and negative = hydrophilic. Scale goes from +4.5 (Ile) to -4.5 (Arg). Think of it as related to the change in Gibbs free energy in moving the amino acid from non-polar solvent (acetone) to water. Draw bar to the far right. GROUP 1; NON-POLAR, ALIPHATIC (OFTEN HYDROPHOBIC) G,A,V,L,I,P

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 4 Glycine; Gly, G, – 0.4 Smallest amino acid. Not terribly hydrophobic. No acid/base groups, no potential H- bonding groups, not especially reactive. Alanine; Ala, A, 1.8 Properties much like glycine, but more hydrophobic. Valine; Val, V, 4.2 "V-shaped". Very hydrophobic. Leucine; Leu, L 3.8 "Like val only Longer". Hydrophobic. Isoleucine; Ile, I 4.5 "Isomer of leucine". Most hydrophobic of all amino acids. Proline; Pro, P -1.6 The only cyclic amino acid. Somewhat hydrophilic. Constrained movement around peptide bond; puts kink in proteins; we'll discuss this point later. GROUP 2; POLAR, UNCHARGED S,T,C,M,N,Q

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 5 Serine; Ser, S -0.8 Not charged, but polar because of OH group; good hydrogen bonder; often in active sites because good e - -phile. pK a not in the physiol. pH range, not deprotonated under normal circumstances. (13.6) Threonine ; Thr, T -0.7 Much like S, but not often at enzyme active site. Cysteine; Cys, C 2.5 Sort of a Ser analog, but not so good a H-bonder because electronegativity of O > that of S. pK a beyond physiol pH range. (10.3) The S can be oxidized, and then linked to another to form a disulfide bridge. In this configuration, it is called Cystine. Can hook distant portions of a protein together, extremely important in stabilizing protein structure. Can be reduced to two Cys's again. Methionine, Met, M , +1.9 Called "thiol-like". Always the first amino acid added to start protein synthesis, initiator codon (often removed in eukaryotes, modified in prokaryotes). Hydrophobic. Asparagine, Asn, N , -3.5 Amine of aspartate (we'll see). Good H-bonder. Not a nucleophile of acid/base because the e - is shared by the O and N.

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